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All posts created by aajohnson

| posted 11 May, 2024 14:01
Awesome thank you!!
Posted in: Request a new function on the SEA-PHAGES official listanti-CBASS type III-C protein
| posted 06 May, 2024 19:37
Hi!

This is an investigation of function for Balomoji protein #102 (Pecaan) or 102 (final DNAMaster file), genome coordinates 60991-61688, pham 163488.

We answer the required questions and make a pitch in this google doc for consideration of function related to cyclic trinucleotide binding anti-CBASS proteins, inspired by Dr. Bondy-Denomy's SEA Symposium presentation.

Allison and two fantastic students who did this work, Harshini and Mariya
Posted in: Request a new function on the SEA-PHAGES official listanti-CBASS type III-C protein
| posted 12 Apr, 2023 19:57
Thanks Debbie.
Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam:
http://pfam-legacy.xfam.org/family/PF06488.14
with 90% probability in HHPred, coverage of 74% (and a terrible evalue).

Allison
Posted in: Cluster EC Annotation TipsMajor tail protein
| posted 12 Apr, 2023 19:57
Thanks Debbie.
Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam:
http://pfam-legacy.xfam.org/family/PF06488.14
with 90% probability in HHPred, coverage of 74% (and a terrible evalue).

AJ
Posted in: Cluster EC Annotation TipsMajor tail protein
| posted 12 Apr, 2023 19:57
Thanks Debbie.
Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam:
http://pfam-legacy.xfam.org/family/PF06488.14
with 90% probability in HHPred, coverage of 74% (and a terrible evalue).

AJ
Posted in: Cluster EC Annotation TipsMajor tail protein
| posted 12 Apr, 2023 19:57
Thanks Debbie.
Is 90% probability hit to a pfam ok for functional annotation? LittleFortune gp31 does hit a tail tube pfam:
http://pfam-legacy.xfam.org/family/PF06488.14
with 90% probability in HHPred, coverage of 74% (and a terrible evalue).

AJ
Posted in: Cluster EC Annotation TipsMajor tail protein
| posted 05 Apr, 2023 18:40
We are trying to figure out how/why the major tail protein (LittleFortune gene 31, pham 74364, sequence file attached) is annotated with this function in Microbacteriophages. There is no functional annotation evidence support through blastp CDD or HHPred. The Microbacteriophages paper (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0234636) describes the major tail protein twice, such as "and the major tail protein gene is atypically located upstream of some of the head-to-tail connector genes". Some maps have this label on a protein, we just can't figure out where this label is coming from. Point me in the right direction please?
Posted in: Cluster EC Annotation TipsMajor tail protein
| posted 23 Feb, 2023 13:40
Perfect, thank you.
Posted in: Functional AnnotationRefSeq and INSDC name disagreements in NCBI Blast for Functonal Assignment
| posted 22 Feb, 2023 20:25
This was useful today! Thank you.
Posted in: Cluster EC Annotation TipsTail Assembly Chaperone in KaiHaiDragon
| posted 22 Feb, 2023 20:00
debbie
Hi Kyle,
So if you continue to investigate, there is no supporting data for a minor tail protein except NCBI said so. there is no way that a functional call can be made from the blast data that HHPred data sources does not support."

We're getting no blastp CDD or HHPred support for at least two "minor tail proteins" in cluster K phages, including in the publication supplementary tables posted there. I would call them as hypothetical protein. I haven't dug yet for any synteny rules or something related to these- can you point me towards something to use?
I commiserate with you Kyle.
Posted in: Functional AnnotationRefSeq and INSDC name disagreements in NCBI Blast for Functonal Assignment